A colony is also just a normal civ, but with a special relation to the master. Nothing else, besides the appearance in the middle of the game, is special.
Edit: It seems my memory is indeed in error--when I generated a new map the script included 0-39 slots. However, I was right about something else--judging by Bob's readme and other threads, it is not a good idea to start with more than 34 slots filled. Some even say to start with no more than 32.
Fortunately, this leads me to propose a new solution that isn't too far off from what I said in the first place. For those of you who are getting Instant Defeat, do not put starting coordinates in empty slots. My test .wbs proceeds without them.
I then deleted the last six empty slots, 33-39, so the .wbs only supported 34 players. The test map still loaded successfully under the 40-civ .dll, and I was able to play. This may be an alternative solution--and is also what I had done with my earlier maps. That's what got tangled in my mind. I confused what I had done with what the mod can do. This teaches me to confirm before I speak.
It may be that without those six extra slots specified in the .wbs that colonies cannot be added if the max of 34 civilizations is chosen at start. But if the .dll accomodates 40 civ slots, then it is possible that creating a colony in-game will add a slot, up to the hard max of 40. This will take me a while to figure out, since I haven't tried to run this many civs on my upgraded computer.